vhd-mms/tutorial/base/intro- copertina l.guglielmi - f.pinciroli v isible h uman d ataset - m ilano...

vhd-mms/tutorial/base/intro-copertina

L.Guglielmi - F.Pinciroli

VISIBLE HUMAN DATASET - MILANO MIRROR SITE®

vhd-mms/tutorial/base/intro-1.1-1/2

Visible Human Projectthe idea...

1987 - The National Library of Medicine long time working draft contains the following item:(NLM should)..”thoroughly and systematically investigate the technical requirements and feasibility of instituting a biomedical images library”


Visible Human Projectthe idea...

1988 - During a meeting about 3D anatomical images, held at the NLM Lister Hill National Center for Biomedical Communications, the present people recommend NLM to phisically contribute to the progress of the applicative fileld, directly supporting the development of a image data base of an entire male and female body.

The Visible Human Project Idea

vhd-mms/tutorial/base/intro-1.2

Visible Human Projectthe evolution...

1989 - NLM Board of Regents starts a study to evaluate the role of NLM inside the field, instantly variable, of Electronic Imaging.

1990, April - NLM Board of Regents approve a report that textually said:(The)”NLM should undertake a first project, building a digital image library of volumetric data representing a complete normal adult human male and female”


Visible Human Projectthe announcement...

1991 - NLM agreed with some medicals of the Colorado University with the aim to search for a good cadaver, and for acquiring the images needed by the project.

1994, November 28 - NLM give the announcement of complete availability of a data set containing digital images of male anatomy.


Visible Human DataSet CT and MR images acquisition

Because pilot studies prove that CT and MR images could have a degradation because the body freezing operations, the images, where applicable, are been taken before this frozen procedure MR images acquisition at Colorado University

Hospital (male)

format: General Electric Genesis 256x256x16-bit matrix

operations start: 18 hours after dead operations end : 21.75 hours after dead storing: via ethernet to the Medicin School of the Colorado University,

and then directly on 4-mm DAT cartridges



CT images acquisition need to immobilize the cadaver with a shape-retaining plastic material CT images acquisition at Colorado

University Hospital (male)

step dimension: 1/3/5-mm operations start : 22.5 hours after dead operations end : 25.5 hours after dead



Freezing of the cadaver operations start: 26 hours after death put into a special freezing chamber until October, 15 1993

moving to another maintaining freezing cell with constant temperature of -7°C

Frozen CT images acquisition spacing of 1-mm first step: (head to midcalf) August, 29 1993 second step: (midcalf to toes) October, 14 1993

Male


Visible Human DataSet Tecnica di fotografia

All the slices photographed in red, green and blue (RGB)

All the photos in the 3 tonality (together forming the fullcolor version) has been acquired in TIFF format 2048x2048x14-bit (“raw images”)


Visible Human Project Male choice

Search for the cadavers setup of a consortium of SABs (State Anatomical

Board) of Colorado, Texas and Maryland. Human bodies that become available for medical research and teaching are btained in mosta states through gifts by their citizens to the SAB.

inventory of a lot of possible cadaver, divided by sex, and setup of a screening process reviewed all the medical records of each candidate

cadaver final choice


Visible Human Project Male choice

Cadaver setup dead at 12:31 AM on August, 5 1993

(by court-ordered lethal injection at the Texas Department of Corrections in Huntsville)

body reaches the SAB of Texas about 1.5 hours later final tests and cadaver setup (previous exams had showed the

“normality” of the candidate; only an appendectomy at age 21 and a left orchiectomy at age 15; number 14 teooth had been extracted at age 38)

body reaches the SAB of Colorado about 8 hours after death

at 12.5 hours after death were obtained and later digitized 15 radiographs


Visible Human DataSet Final Male choice

September, 2 1993 NLM’s Visible Human Project Selection Panel, made up of anatomists and radiologists discuss about CT and MR images of two anonymous cadaver. The panel decided unanimously to proceed with SAB number 6022 as the Visible Human Male. So it gave start to all the technical procedures need for sectioning the cadaver and acquiring relative further images.


Visible Human DataSet Female choiceCharacteristics

Death: September, 1993Motivazione: Arresto cardio-

polmonareHousewifeEtnia caucasica58 years old


Visible Human DataSet Female choice General conditions

No fracture or subluxationStandard bony mineralizationBilateral degenerative variations at

L4-5 and L5-S1 levelMinimum degenerative variations present at cervical

levelFeet show a contraction, but they don’t seem

abnormsVentricles have normal dimensions


Visible Human DataSet Sectioning of the cadaver

The cutting system was developed at the University of Colorado Medical School in the former Department of Anatomy The machine consisted of a milling device whose controls had

been automated and drives upgrated to retain accuracy when subjected to the intense cold

Cutting blade:disk of 14 inches in dieameter20 specially hardened teeth mounted around its edgespeed rotation: 300 rpm it succesfully shaved blocks containing tissues to 0.1-mm intervals

Male



On January, 20 1994, the cadaver was transfered from the walk-in freezer (-7°C) to the freezing chamber (-70°C). After 2 days, the cadaver was removed from the freezing chamber.

On January, 24, 1994, the frozen cadaver, immobilized in its Alpha Cradle mold, was positioned and clamped to the bed of the backsaw. The initial 4 blocks obtained consisted of:

legs, ankles and feet thighs and knees abdomen and pelvis head, neck and thorax

The kerf loss between them was approximately 1.5 mm

Male



Each block was embedded in a suitable medium, which when frozen would provide stability for the cutting process

Once the gelatine was solid, the mold was transferred to the Ultra Freezer (-85°C) for at least 12 hours. The mold was then removed and partially disassembled. Mold was finally reassembled, with another layer of gelatine siphoned into it. When the final layer was solid, the mold was again transferred to the Ultra Freezer for complete freezing and storage.

Cutting operations start: February, 17 1994 end: May, 19 1994

Male

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The Female dataset, instead of the Male one, has a different sectioning step along the Z direction.

Female sectioning step = 0,33-mm Male sectioning step = 1-mm

Female



The initial 4 blocks obtained consisted of:

1st head, neck and thorax 2nd abdomen and pelvis 3rd thighs and knees 4th legs, ankles and feet

Female


Visible Human DataSet Alignment of

CT/MR/Fullcolor’s images

Individual fullcolor, CT and MR images have been analyzed to establish the correspondence between them, to provide anatomic alignment.(The number of the images are not the same for all the three types, and something has been lost in kerf)

Anatomic and CT slices wer renumbered to reflect the correspondence, starting at 1,001 and proceeding to 2,878. The MR images were renumbered to reflect some anatomic correspondence to the CT and anatomic slices.

vhd-mms/tutorial/base/intro-2.6.1

Visible Human DataSet Digital image processing

All digital images were reduced from 42-bit (14 bits of red, green and blue) to 24-bits images by independently and logarithmically compressing the 14bits of each channel to 8 bits.

The images were cropped in the anteroposterior (AP) dimension of the anatomy from 2,048 to 1,216 pixels.

Male


Visible Human DataSet Data format

Fullcolor: 24-bit “raw” file formatCT: General Electric Genesis format

Fresh Frozen

MR: General Electric Genesis format

Male

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Visible Human DataSet Dataset content

MRI images: axial of head and neck spacing of 4-mm coronal of the body spacing of 4-mm 256x256 pixels (12 bits of gray per pixel) General Electric format

CT images: axial spacing of 1-mm 512x512 pixel (12 bits of gray per pixel) General Electric format

Male



FULLCOLOR images: axials (aligned with the CT ones)

spacing of 1-mm for manspacing of 0.33-mm for woman

(more than 5,000 images only for the anatomic dataset)

2048x1216 pixel (24 bits of color per pixel) raw format, UNIX compressed (e.g.

xxx.raw.Z)

Male



Fullcolor images

Resolution : voxel 0.33mm (same spacing on all the 3 dimensions)

Photographic format: TIFF (with 14 significative bits per RGB

channel)

Images format: raw format 24-bit (8bits per RGB channel)

Female



Characteristics

Fullcolor images: block 1 (head, neck, thorax)

2048x2048x14 bit x RGB TIFF Format blocks 2,3,4 (the other ones)

2048x1280x14 bit RGB TIFF Format except: first 34 images of the block 2 (abdomen and

pelvis)

1760x1280x14bit RGB TIFF Format

Female



X-Ray, CT and MRI images

MRI Format: General Electric Genesis format 256x256x16 bits

CT Format: General Electric Genesis format spacing of 1mm

X-Ray Format: TIFF

Female


Visible Human DataSet Dataset dimensions

Man: about 15 GigaBytes

Woman: about 40 GigaBytes


Visible Human DataSetFullcolor example

Male


Visible Human DataSetCT fresh cadaver example

Male


Visible Human DataSetCT frozen cadaver example

Male


Visible Human DataSetMRI example

Male


Visible Human DataSetexample of a visualization application


Visible Human DataSet Data set access

Via Internet with FTP

Acquired on cassettes (both 4mm or 8mm)

Directly form the National Library of Medicine(http://www.nlm.nih.gov/visible/visible_human.html)

http://www.nlm.nih.gov/visible/visible_human.html
















Visible Human DataSet Dataset amministrative access

Signature of a License Agreement directly with the Nationa Library of Medicine assignment of a couple of userid/password to grant the access to the dataset via FTP

on the NLM server (free access)(Free contract download)

delivery of the dataset on cassettes (by explicit request) (only charge mail expense and hardware support)

Directly from the National Library of Medicine(http://www.nlm.nih.gov/visible/visible_human.html)

http://vhd-mms.cilea.it/nlm.htm






http://vhd-mms.cilea.it/vhpagree.txt



















Visible Human Dataset - Milano Mirror Site®

Motivations To solve all the problems European continental users had to download the data directly from

NLM, due to network constrictions To offer a repository service for all the applications built using Visible Human Project data set To offer to the dataset users a simple, powerful and quick interface to find the data they neeed To establish an European reference point for the NLM Visible Human Project To found a reference and development point for applications based upon VHD


A official continental Europe copy of the entire datasets present on NLM servers A official continental Europe copy of the entire datasets present on NLM servers Male dataset : about 15 GigaBytes Female dataset : about 40 GigaBytes

Storing the entire datasets on RAID disks (about 60 GigaBytes!) for on-line download WEB interface to the data, downloadable via FTP European reference and help desk point for who need informations about VHD download and

use


Goals


Agreeement between Politecnico of Milano (Department of BioEngineering) and CILEA (Consortium of the Italian NorthWest Universities) for the setup and the maintenance of the Continental Europe VHD mirror site


Promoters

http://vhd-mms.cilea.it/cilea.htm

http://vhd-mms.cilea.it/politecnicoMI.htm


Sponsorships to maintain the VHD-MMS services at very high level of quality


Sponsors

http://vhd-mms.cilea.it/bracco.htm

http://vhd-mms.cilea.it/imation.htm

http://vhd-mms.cilea.it/hp.htm

http://vhd-mms.cilea.it/telecom.htm


Availability on-line 365 day/year of all the datasets, storing them on SCSI disk with RAID technology (ca 60Gb)

WEB interface also for FTP download process Excellent network access for European and Italian users

on a GARR node (Italian academic network) near a gateway between GARR and commercial ISPs near the main commercial ISPs italian gateway point


Technical criteria


• HP Netserver LX PRO• Bi-processor Pentium 200• 9 disks RAID, each one of 9Gb

• SCO UNIX Open Server• Netscape Web Fasttrack Server


Hardware/Software


Internet

VHD-MMS

GARR

NAP #n

2Mb/s

512Kb/s

NSP #n

NAPNAPCILEACILEA

MIX

NSP #n

NSP #n> 34Mb/s

>8Mb/s

2Mb/s


Internet connection



Web site


Coordinator

Prof. Francesco Pinciroli Tel. (39) (2) 2399.3335

e-mail: [email protected].

it

Technical Manager

Dott. Luciano Guglielmi Tel. (39) (2) 26995.267

e-mail: [email protected]

Informations: [email protected]

http://vhd-mms.cilea.it/

Services of the Visible Human Dataset - Milano Mirror Site®

Qualified and continuos help desk

mailto:[email protected]




























http://vhd-mms.cilea.it/ftp://[email protected]

Services of theVisible Human Dataset - Milano Mirror Site®

Continuos accessaccess to the data via FTPvia FTP,

also using a WEB interface











ftp://vhd-mms.cilea.it/











vhd-mms/tutorial/base/intro-4.5.3.1


To scrape together products based on the “Visible Human Dataset” based

products

Built of a collection of VHD based product at the Library of the Department of BioEngineering of the Politecnico di Milano, made available both from single editors or found on the marketWeb access to this repository for queries about availability and borrow purpose, will be ready as soon as possible.



Web Site VHD-MMS in all the European language

Availability of the Visible Human Dataset - Milano Mirror Site®

Web site in all the European languages


Services offered byVisible Human Dataset - Milano Mirror Site®

Disk space availability for storing, and delivering via internet, any kind of

applications built using the Visible Human Dataset

(with special attention to those made up by individuals or groups coming from continental Europe)

availability confirmedwaiting for requests...



Money and logistic contribution

Contribution assignment, both money and logistic

ones,

with the goal to promote scientific PhD and university

degree works, based on the use of the VHD and the

optimization of the services offered by the




”Help us to serve you better…”

Setup of a direct web line with the users, to collect:

Advices RemarksCriticisms

SuggestionsAppreciations

vhd-mms/tutorial/base/intro- copertina l.guglielmi - f.pinciroli v isible h uman d ataset - m ilano...

Documents

visible human dataset

dead slide

visible human dataset

digital images of male

female slide

d anatomical images

dead x operations end

role of nlm